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Parallel Computing Research

Parallel Computing Research. L.V. (Sanjay) Kale Professor Dept. of Computer Science http://www.ks.uiuc.edu/Research/namd. Overview. Research at PPL Develop technology that improves: performance of parallel applications programmer productivity Load balancing issues

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Parallel Computing Research

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  1. Parallel Computing Research L.V. (Sanjay) Kale Professor Dept. of Computer Science http://www.ks.uiuc.edu/Research/namd

  2. Overview • Research at PPL • Develop technology that improves: • performance of parallel applications • programmer productivity • Load balancing issues • Communication optimizations • Parallel algorithms • Collaboration: CSE applications

  3. Protein Folding Quantum Chemistry (QM/MM) Molecular Dynamics Computational Cosmology Charm++ Parallel Objects, Adaptive Runtime System Libraries and Tools Crack Propagation Dendritic Growth Space-time meshes Rocket Simulation Enabling CS technology of parallel objects and intelligent runtime systems has led to several collaborative applications in CSE

  4. Charm++ in wider use • Applications are using Charm++ • Adding to its stability, robustness • Rocket simulation (ASCI center) • Computational Cosmology (Astrophysics) • QM (Car-Parinello method) • Crack propagation • Space-time meshes in process simulation • Large data visualization

  5. Blue Gene • Blue Gene/L • 64K dual processor nodes • Targeted peak performance 180/360TF/s • Simulation and performance prediction • Demonstrated efficient parallelization of skeletal MD program

  6. Collective Communication • Performance impediment • Issues • Communication latencies not scaling with bandwidth and processor speeds • High software over head (α) • Synchronous operations (MPI_Alltoall) do not utilize the co processor effectively • All to all personalized communication • Each processor has P messages to send • Dominated by software overhead

  7. Optimizing AAPC • Message combining for small messages • Reduce the total number of messages • Messages sent along a virtual topology • Multistage algorithm to send messages • Group of messages combined and sent to an intermediate processors which then forward them to the final destinations • Using virtual topologies reduces software overhead of sending messages

  8. Virtual Topology:Mesh Organizeprocessors in a 2D (virtual) Mesh Message from (x1,y1) to (x2,y2) goes via (x1,y2) 2* messages instead of P-1

  9. Namd Performance on Lemieux

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